LXL04_026422 | RubberDandelionOmics

Gene overview

LXL04_026422

Reference: OH-1004 Chr: Chr05 Coordinates: 126082575-126086725 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2316 bp · LXL04_026422|LXL04_026422|OH1004|cDNA

ATGTGTTTGCTCACAGGTGATAAAAGTGGGAGACCTAGCAAGAAGCACAAATCATCATCATCCAAGGATGACTATAGAGCTGCAGCGTTTGAAGAAGAGGAAGCATATTATGCTGAAGAATTTGGTGATGATGATCGTGATGGAGATGGAGAAGGCAAAAAGAGAGATTTTACAAAATTGGAACTTAAAGCAGATCACGTGAATCGACCATTATGGGCCTGTGCAGATGGTCGAATATTTCTAGAAACATTTTCTCCGTT...

CDS

Download CDS FASTA

2316 bp · LXL04_026422|LXL04_026422|OH1004|CDS

ATGTGTTTGCTCACAGGTGATAAAAGTGGGAGACCTAGCAAGAAGCACAAATCATCATCATCCAAGGATGACTATAGAGCTGCAGCGTTTGAAGAAGAGGAAGCATATTATGCTGAAGAATTTGGTGATGATGATCGTGATGGAGATGGAGAAGGCAAAAAGAGAGATTTTACAAAATTGGAACTTAAAGCAGATCACGTGAATCGACCATTATGGGCCTGTGCAGATGGTCGAATATTTCTAGAAACATTTTCTCCGTT...

Protein

Download Protein FASTA

771 aa · LXL04_026422|LXL04_026422|OH1004|PROTEIN

MCLLTGDKSGRPSKKHKSSSSKDDYRAAAFEEEEAYYAEEFGDDDRDGDGEGKKRDFTKLELKADHVNRPLWACADGRIFLETFSPLYKQAYDFLIAIAEPVCRPESMHEYNLTPHSLYAAVSVGLETETIISVLNKLSKTKLPKEMIDFIHASTANYGKVKLVLKKNRYLVESPFPDVLKRLLSDEVISRARISSEMGDDGFSVSRSAGEIDGRHEELLTEAQLAAAAEEKEAHSFEIDPAQVENVKQRCLPNALNYPM...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_026422`
TK1151 ID	TkA06G012430
OH-1004 ID	LXL04_026422
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 99.610 / OH-1004 99.351 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_026422

Location Chr05:126082575-126086725 (-)

Description Similar to XPB1: General transcription and DNA repair factor IIH helicase subunit XPB1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g41370`	ATP-dependent 3'-5' DNA helicase/translocase; binds dsDNA rather than ssDNA, unzipping it in a translocase rather than classical helicase activity (By similarity).	The participation of AtXPB1, the XPB/RAD25 homologue gene from Arabidopsis thaliana, in DNA repair and plant development.2001 · DOI: 10.1046/j.1365-313x.2001.01162.x
`At5g41360`	ATP-dependent 3'-5' DNA helicase/translocase; binds dsDNA rather than ssDNA, unzipping it in a translocase rather than classical helicase activity (By similarity).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026422 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006265 DNA topological change Biological Process

GO:0006281 DNA repair Biological Process

GO:0006283 transcription-coupled nucleotide-excision repair Biological Process

GO:0006289 nucleotide-excision repair Biological Process

GO:0006362 transcription elongation by RNA polymerase I Biological Process

GO:0006366 transcription by RNA polymerase II Biological Process

GO:0006367 transcription initiation at RNA polymerase II promoter Biological Process

GO:0006974 DNA damage response Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0008104 intracellular protein localization Biological Process

GO:0009411 response to UV Biological Process

GO:0009650 UV protection Biological Process

KEGG gene cross-reference

ath:AT5G41360

ath:AT5G41370

ddi:DDB_G0278729

dre:324323

mmu:13872

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.945

Rank 1 · LXL04_026422 · OH-1004

Cytoplasm0.116

Rank 2 · LXL04_026422 · OH-1004

Mitochondrion0.020

Rank 3 · LXL04_026422 · OH-1004

Cell membrane0.019

Rank 4 · LXL04_026422 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_026422 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF13625.12Helicase_C_371-194 aa

PF04851.22ResIII284-441 aa

PF16203.12ERCC3_RAD25_C466-712 aa

PF00271.38Helicase_C516-618 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026422	`PF13625.12`	Helicase_C_3	71	194	6.3e-34	117.4
LXL04_026422	`PF04851.22`	ResIII	284	441	5.9e-18	66.0
LXL04_026422	`PF16203.12`	ERCC3_RAD25_C	466	712	2.5e-116	388.0
LXL04_026422	`PF00271.38`	Helicase_C	516	618	1.1e-13	52.0

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q38861`	Arabidopsis thaliana	General transcription and DNA repair factor IIH helicase/translocase subunit XPB1	87.320%	Swiss-Prot	strong database homology
`Q9FUG4`	Arabidopsis thaliana	General transcription and DNA repair factor IIH helicase/translocase subunit XPB2	84.695%	Swiss-Prot	strong database homology

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